Is it possible to retrieve flanking sequence at the 5' and/or 3' ends of IMGT labels that describe IMGT/GENE-DB annotated sequences?
Yes, flanking sequences at the 5' and/or 3' ends of the IMGT labels can be retrieved, in FASTA format,
by querying the IMGT/GENE-DB entry section, "Choose your display > IMGT label extraction
from IMGT/LIGM-DB reference sequences".
For more information: IMGT label extraction
from IMGT/LIGM-DB reference sequences.
How can I retrieve the V leader sequences from IMGT reference sequences?
Step 1: Make your selection (species, group, functionality) in
IMGT/GENE-DB
(access from http://www.imgt.org).
For a selection "Homo sapiens", "IGHV" and "functional", the results of your search will be, for example:
Step 2: Select all genes (click in box at the bottom of the list of resulting genes)
and in the "Choose your display" "IMGT label extraction from IMGT/LIGM-DB reference sequences" section,
click on "Choose label(s) for extraction" and select the IMGT label "L-PART1+L-PART2"
(L-PART1 and L-PART2 being shown as artificially spliced in that query).
How to obtain from IMGT/GENE-DB complete sequences of a constant gene, or of a group of C genes?
To get the complete amino acid sequence (artificially spliced) of a reference constant gene, the query is 13.2
http://www.imgt.org/genedb/GENElect?query=13.2+Genesymbol&species=Species
with for Genesymbol, the gene name (for instance IGHG1), and for Species, the latin name of the species (for instance Homo+sapiens)
http://www.imgt.org/genedb/GENElect?query=13.2+IGHG1&species=Homo+sapiens
To get the artificially spliced nucleotide sequence of that gene, the query is 13.1
To get the complete amino acid sequence (artificially spliced) of reference constant genes of a group, the query is 14.2
http://www.imgt.org/genedb/GENElect?query=14.2+Group&species=Species
with for Group, the group name (for instance IGHC), and for Species, the latin name of the species (for instance Homo+sapiens)
http://www.imgt.org/genedb/GENElect?query=14.2+IGHC&species=Homo+sapiens
To get the artificially spliced nucleotide sequence of that group, the query is 14.1
The information on the direct links are available at: http://www.imgt.org/genedb/directlinks
You can access that page at the bottom of the IMGT/GENE-DB Query page.
How to download the sequences of the available IG or TR genes of a given group of a given species, for example Homo sapiens IGHV, from IMGT/GENE-DB?
For the download of sequences, you may query the database:
in the IMGT/GENE-DB Query page, IDENTIFICATION: Species= Homo sapiens, CLASSIFICATION: IMGT group= IGHV.
At the bottom of the 'RESULTS OF YOUR SEARCH PAGE', click on "Select all genes",
and in the section "Choose your display" (see http://www.imgt.org/genedb/doc#h2_62)
select one of the options of "IMGT/GENE-DB allele reference sequences in FASTA format".
An alternative is to use an URL with format described in the direct links (http://www.imgt.org/genedb/directlinks), for example:
http://www.imgt.org/genedb/GENElect?query=7.2+IGHV&species=Homo+sapiens
How to retrieve sequences of the alleles of the human constant genes?
You can retrieve nucleotide and amino acid sequences of the alleles of a given gene in IMGT/GENE-DB (http://www.imgt.org/genedb/),
from the table 'IMGT/GENE-DB reference sequences (in FASTA format)' displayed in the 'IMGT/GENE entry' page resulting from the query
(for instance, Homo sapiens IGHG1).
You can retrieve nucleotide or amino acid sequences for a given gene (e.g., IGHG1 gene) or for genes of a group (e.g., IGHC group) of a given species (e.g., Homo sapiens), using the IMGT/GENE-DB direct links (http://www.imgt.org/genedb/directlinks).
Alleles can be compared visually in 'Alignments of alleles' (http://www.imgt.org/IMGTrepertoire/Proteins/index.php#B) in IMGT Repertoire.
